CATH Documentation

This secondary structure alignment program uses dynamic programming to align proteins by matching vectors between residues. For each residue in a protein, a local
structural environment is defined by a set of inter-atomic vectors. The method
matches residues by comparing these structural environments. An important aspect
of these environments is that because they are defined independently for each
residue, they are rotationally invariant, making their comparison insensitive
to the displacement of substructures. This method also allows other residue
properties to be included in the comparison, including solvent accessible
area and torsional angles (corresponding to degree of burial and secondary
structure), thus improving the alignment of remote protein structures. An important
advantage of this method is that it is completely automatic. This algorithm is used to
cluster structurally similar proteins in the CATH system.